OBO-Edit: Help document OBO-Edit 2: Difference between revisions

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There are many differences between OBO-Edit 1 and OBO-Edit 2. The OBO-Edit User Guide refers to version 1, and needs to be substantially revised before we can release OBO-Edit 2 to the public.
[[Category:OBO-Edit]]
(Updated 19 Aug 2008)
(Updated 13 March 2009)


OBO-Edit users, we need your help!  <b>Please add your name to the section or sections to which you are willing to contribute.</b>  Feel free to add new sections to the list as well--this is definitely not a complete list. Don't worry about formatting or polishing your text.  Just send whatever you have to Nomi, and she'll take care of making it pretty.
These are the help pages that still need to be updated (or, in some cases, written):


* Drag and drop layout customization
*The_OBO_Adapter.htm - has dead link to root picking, which is no longer part of the filtering documentation
* Creating new layouts (and other general layout management) Jen: DONE
* The OBO OWL Adapter (empty page; not yet linked from index)
* The new search system
* The OWL URL Reader (empty page; not yet linked from index)
**Term search Jen: DONE
* The GO Association File Adapter (empty page; not yet linked from index)
**Link search Jen: some screenshots sent in but still fairly confused about how this works. There is some good develop documentation on the link filter but I can't find it now. Still searching for it.  
* Graph Viewer - review to confirm accuracy, especially the bit on "succinct" (or whatever we end up calling it)
* The new rendering system (particularly the html expression syntax)
* Graph_Editor.htm ? (or has this been done since Aug '08? -mah)
** html expression syntax Jen: basic stuff DONE
* Importing_Terms.htm (empty page; not yet linked from index)
** would be useful also to have simpler version of [http://wiki.geneontology.org/index.php/OBO-Edit:_Arcana_for_User%27s_Guide John's Guide]
* The_ID_Fixer.htm (empty page; not yet linked from index)
* Configurable Message Jen: DONE-ish - with rather lame example.
* All of the Reasoner pages (maybe some are ok as-is, but they all need to be looked at)  
* Reasoner, cross products (xps):  Chris M.
* Semantic_Parser_Manager.htm (empty page)
* Help for individual components: Nomi
* Cross_Product_Matrix_Editor.htm (nearly empty page)
* User-configurable heat maps
* Expressions pages  (may be ok as-is, but they all need to be looked at)
* Hotkey system (see [http://sourceforge.net/mailarchive/forum.php?thread_name=BEB35549-C4BB-4346-A499-8D85B22FF2AB%40berkeleybop.org&forum_name=geneontology-oboedit-working-group John's summary]) Midori
* The Command Line pages  (may be ok as-is, but they all need to be looked at)
* Table of Contents: Jen: DONE.
 
* Annotation Summary Component: Jen - I do not know how to work this.  
Additions March 16-18, 2009
* Term Image Display Panel: Jen: DONE
 
<br>
* Loading_a_History_File.htm - check for accuracy, especially in light of [https://sourceforge.net/tracker/index.php?func=detail&aid=2526247&group_id=36855&atid=418257| SF 2526247] bug report
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* The_Reasoner_and_the_Interface.htm seems to need some updating, at least to add the RuleBasedReasoner, add a link to the Reasoner Manager help page, and maybe decrease redundancy with the reasoner manager page (also, the note in parentheses at the beginning seems out of place)
* The_Reasoner_Manager needs updating - add experimental RuleBasedReasoner
* Reasoner_Prefilters needs updating - still mentions the old "flower button"
* I've done a modest update on Cross_Products_in_the_Text_Editor.htm, and the intro to xps is pretty general and therefore probably OK. But these cross-product pages need attention (if we're keeping the features they refer to ...), even if just to confirm that they're OK:
** Cross_Product_Matrix_Editor.htm (also noted in old list above)
** Cross_Product_Info.htm
** Intersection_Editor.htm
* Plugins.htm - a programmer should check over this one
* I think the command line pages are probably OK, but it won't hurt for one or two others to take a look.


Some references that might be useful:
(midori)
== Some references that might be useful: ==


* [http://www.oboedit.org/docs/ User Guide for OBO-Edit 1]
* [http://www.oboedit.org/docs/ User Guide for OBO-Edit 1]
* [[OBO-Edit_2.000_Testing_Tasks]] outlines much of the GUI functionality of OE2
* [[OBO-Edit_2.000_Testing_Tasks]] outlines much of the GUI functionality of OE2
* The [[OBO-Edit 2.0 beta release notes]] mention some of the differences between OE1 and 2.
* The [[OBO-Edit 2.0 beta release notes]] mention some of the differences between OE1 and 2.
* The [http://sourceforge.net/mailarchive/forum.php?forum_name=geneontology-oboedit-working-group OBO-Edit Working Group] mailing list archives may also be useful, particularly the WG weekly chat transcripts
* The [http://sourceforge.net/mailarchive/forum.php?forum_name=geneontology-oboedit-working-group OBO-Edit Working Group] mailing list archives may also be useful, particularly the WG weekly [[Web_chat_transcripts|chat transcripts]]
* Browse the SourceForge SVN [http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/ code repository] (which includes the oboedit code and also the code for the bbop and obo libraries that oboedit uses)
* Browse the SourceForge SVN [http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/ code repository] (which includes the oboedit code and also the code for the bbop and obo libraries that oboedit uses)
* John put together a page with some [http://wiki.geneontology.org/index.php/OBO-Edit:_Arcana_for_User%27s_Guide bits of arcana about OE 2]


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Return to [[OBO-Edit]] main page
Return to [[OBO-Edit]] main page

Latest revision as of 15:28, 30 June 2014

(Updated 19 Aug 2008) (Updated 13 March 2009)

These are the help pages that still need to be updated (or, in some cases, written):

  • The_OBO_Adapter.htm - has dead link to root picking, which is no longer part of the filtering documentation
  • The OBO OWL Adapter (empty page; not yet linked from index)
  • The OWL URL Reader (empty page; not yet linked from index)
  • The GO Association File Adapter (empty page; not yet linked from index)
  • Graph Viewer - review to confirm accuracy, especially the bit on "succinct" (or whatever we end up calling it)
  • Graph_Editor.htm ? (or has this been done since Aug '08? -mah)
  • Importing_Terms.htm (empty page; not yet linked from index)
  • The_ID_Fixer.htm (empty page; not yet linked from index)
  • All of the Reasoner pages (maybe some are ok as-is, but they all need to be looked at)
  • Semantic_Parser_Manager.htm (empty page)
  • Cross_Product_Matrix_Editor.htm (nearly empty page)
  • Expressions pages (may be ok as-is, but they all need to be looked at)
  • The Command Line pages (may be ok as-is, but they all need to be looked at)

Additions March 16-18, 2009

  • Loading_a_History_File.htm - check for accuracy, especially in light of SF 2526247 bug report
  • The_Reasoner_and_the_Interface.htm seems to need some updating, at least to add the RuleBasedReasoner, add a link to the Reasoner Manager help page, and maybe decrease redundancy with the reasoner manager page (also, the note in parentheses at the beginning seems out of place)
  • The_Reasoner_Manager needs updating - add experimental RuleBasedReasoner
  • Reasoner_Prefilters needs updating - still mentions the old "flower button"
  • I've done a modest update on Cross_Products_in_the_Text_Editor.htm, and the intro to xps is pretty general and therefore probably OK. But these cross-product pages need attention (if we're keeping the features they refer to ...), even if just to confirm that they're OK:
    • Cross_Product_Matrix_Editor.htm (also noted in old list above)
    • Cross_Product_Info.htm
    • Intersection_Editor.htm
  • Plugins.htm - a programmer should check over this one
  • I think the command line pages are probably OK, but it won't hurt for one or two others to take a look.

(midori)

Some references that might be useful:


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